Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012676.1 Kokia drynarioides strain JFW-HI SEQ_127687, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 300401
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 110 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:275414 original size:6 final size:6
Alignment explanation
Indices: 275403--275442 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
275393 AATCTAACTT
*
275403 AAAATA AAAATA AAAAT- AAAATA AGAATA AAAATA AAAAT
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT
275443 GATTCCAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:275423 original size:11 final size:11
Alignment explanation
Indices: 275402--275440 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
275392 TAATCTAACT
275402 TAAAATAAAAA
1 TAAAATAAAAA
275413 TAAAA-ATAAAA
1 TAAAATA-AAAA
275424 TAAGAATAAAAA
1 TAA-AATAAAAA
275436 TAAAA
1 TAAAA
275441 ATGATTCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.04
11 14 0.56
12 9 0.36
13 1 0.04
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (11 bp):
TAAAATAAAAA
Found at i:275424 original size:17 final size:17
Alignment explanation
Indices: 275402--275440 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
275392 TAATCTAACT
275402 TAAAATAAAAATAAAAA
1 TAAAATAAAAATAAAAA
*
275419 TAAAATAAGAATAAAAA
1 TAAAATAAAAATAAAAA
275436 TAAAA
1 TAAAA
275441 ATGATTCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (17 bp):
TAAAATAAAAATAAAAA
Found at i:278448 original size:5 final size:5
Alignment explanation
Indices: 278438--278468 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
278428 CTGAAAGGAG
*
278438 AAGAA AAGAA AAGAA AAGAA AAGAA CAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
278469 TATCCTCACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.77, C:0.03, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:287977 original size:16 final size:16
Alignment explanation
Indices: 287956--288002 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
287946 TAACAATTTA
*
287956 AATAAATTAAAAAGTT
1 AATAAATTAAAAAATT
287972 AATAAATTAAATAAATT
1 AATAAATTAAA-AAATT
*
287989 AA-AAATTAGAAAAT
1 AATAAATTAAAAAAT
288003 AAATTCTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 4 0.14
16 18 0.64
17 6 0.21
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (16 bp):
AATAAATTAAAAAATT
Found at i:287984 original size:9 final size:9
Alignment explanation
Indices: 287953--287991 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
287943 TATTAACAAT
287953 TTAAATAAA
1 TTAAATAAA
*
287962 TTAAA-AAG
1 TTAAATAAA
287970 TT-AATAAA
1 TTAAATAAA
287978 TTAAATAAA
1 TTAAATAAA
287987 TTAAA
1 TTAAA
287992 AATTAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 2 0.08
8 8 0.31
9 16 0.62
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (9 bp):
TTAAATAAA
Found at i:288221 original size:22 final size:22
Alignment explanation
Indices: 288196--288250 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
288186 CACTCGGTAG
288196 CAACAATAGCAGCACACTTGGA
1 CAACAATAGCAGCACACTTGGA
* *
288218 CAACAGTAGCAGCACTCTTGGA
1 CAACAATAGCAGCACACTTGGA
* *
288240 CAGCAACAGCA
1 CAACAATAGCA
288251 TGCCTAGACA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.29, G:0.20, T:0.13
Consensus pattern (22 bp):
CAACAATAGCAGCACACTTGGA
Found at i:288715 original size:15 final size:14
Alignment explanation
Indices: 288693--288728 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
288683 TGAAATTTTA
288693 AAATAAAAAAAAAT
1 AAATAAAAAAAAAT
*
288707 AACATAAAAATAAAT
1 AA-ATAAAAAAAAAT
288722 AAATAAA
1 AAATAAA
288729 CTTTATTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.17
Consensus pattern (14 bp):
AAATAAAAAAAAAT
Found at i:291606 original size:123 final size:122
Alignment explanation
Indices: 291387--291749 Score: 561
Period size: 123 Copynumber: 3.0 Consensus size: 122
291377 TATCTTTCCT
* * * *
291387 TTTTATTTAATATCTCATATTAAAATGGAAATATTCCTTTTG-GTAAATATATGAAAGATTTATT
1 TTTTATATAATATCTCATATTAAAATGGAAATATTCCCTTTGAG-AAATATATGGAAGGTTTATT
* *
291451 AAAACATTGTATCCTTTCCAATAGGATATTAACTTCCATGTTTTTAATATTTAATTTCA
65 -AAACATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATTTAATTTCA
*
291510 TTTTATATAATATCTCATATTAAAATGGAAATATTCCCTTTGAGAAATATATGGTAGGTTTATTA
1 TTTTATATAATATCTCATATTAAAATGGAAATATTCCCTTTGAGAAATATATGGAAGGTTTATTA
*
291575 AAGCATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATTTAATTTCC
66 AA-CATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATTTAATTTCA
* *
291633 TTTTATATAATATCTCATATTAAAATGAAAATATT-CCTTTAAAGAAATATATGGAAGGTTTATT
1 TTTTATATAATATCTCATATTAAAATGGAAATATTCCCTTT-GAGAAATATATGGAAGGTTTATT
*
291697 AGAACTTTATATCCTTTCCAAAAGGATATTAACTTCCATG-TTTTAATATTTAA
65 A-AACATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATTTAA
291750 CAAAATCATT
Statistics
Matches: 224, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
122 21 0.09
123 200 0.89
124 3 0.01
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.44
Consensus pattern (122 bp):
TTTTATATAATATCTCATATTAAAATGGAAATATTCCCTTTGAGAAATATATGGAAGGTTTATTA
AACATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATTTAATTTCA
Found at i:292512 original size:166 final size:166
Alignment explanation
Indices: 292238--292568 Score: 653
Period size: 166 Copynumber: 2.0 Consensus size: 166
292228 AAGTAGACTA
292238 AAATAAACAAATAAGTGTAATATCTAATATTAACTTATTTGAGCATGACCATGCATTTCTAGTCT
1 AAATAAACAAATAAGTGTAATATCTAATATTAACTTATTTGAGCATGACCATGCATTTCTAGTCT
292303 CACTTCATCAAGTGGCCTAGGATATTGCTCCCATTATGTAGGAGGGACAAATCCTATCTTGATCA
66 CACTTCATCAAGTGGCCTAGGATATTGCTCCCATTATGTAGGAGGGACAAATCCTATCTTGATCA
292368 ATCATATCCCACTACATAGATTGTTGCATACCTATC
131 ATCATATCCCACTACATAGATTGTTGCATACCTATC
292404 AAATAAACAAATAAGTGTAATATCTAATATTAACTTATTTGAGCATGACCATGCATTTCTAGTCT
1 AAATAAACAAATAAGTGTAATATCTAATATTAACTTATTTGAGCATGACCATGCATTTCTAGTCT
*
292469 CACTTCATCAAGTGGCCTAGGATATTGCTCCCATTATGTAGGAGGGACAAATCCTATGTTGATCA
66 CACTTCATCAAGTGGCCTAGGATATTGCTCCCATTATGTAGGAGGGACAAATCCTATCTTGATCA
292534 ATCATATCCCACTACATAGATTGTTGCATACCTAT
131 ATCATATCCCACTACATAGATTGTTGCATACCTAT
292569 TAGTCTCTAT
Statistics
Matches: 164, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
166 164 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (166 bp):
AAATAAACAAATAAGTGTAATATCTAATATTAACTTATTTGAGCATGACCATGCATTTCTAGTCT
CACTTCATCAAGTGGCCTAGGATATTGCTCCCATTATGTAGGAGGGACAAATCCTATCTTGATCA
ATCATATCCCACTACATAGATTGTTGCATACCTATC
Found at i:296903 original size:49 final size:49
Alignment explanation
Indices: 296828--296925 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
296818 AATTCCTTAT
*
296828 TTTTTGCGTTTGAACAAGATAGATACAAGTACTTCGCTTTAGTAGAACC
1 TTTTTGCGTTTGAACAAGATAAATACAAGTACTTCGCTTTAGTAGAACC
296877 TTTTTGCGTTTGAACAAGATAAATACAAGTACTTCGCTTTAGTAGAACC
1 TTTTTGCGTTTGAACAAGATAAATACAAGTACTTCGCTTTAGTAGAACC
296926 CACATTGTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (49 bp):
TTTTTGCGTTTGAACAAGATAAATACAAGTACTTCGCTTTAGTAGAACC
Found at i:298324 original size:123 final size:123
Alignment explanation
Indices: 298176--298534 Score: 578
Period size: 122 Copynumber: 2.9 Consensus size: 123
298166 TATCTTTCAT
* * * *
298176 TTTTATTTAATATTTCATATTAAAATGAAAATATTCCTTTTGAGAAATATATGGAAGGTTTATTC
1 TTTTATATAATATATCATATTAAAATGAAAATATTCCTTTAGAGAAATATATGGAAGGTTTATTA
* * *
298241 AATCATTATATCCTTTCCAAAAGTATATTAACTTTCATGTTTTTAATATTCAATTTCC
66 AAACATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCAATTTCC
* * *
298299 TTTTATATAATATCTCATATTAAAATGAGAATATTCCCTTAGAGAAATATAT-GAAGGTTTATTA
1 TTTTATATAATATATCATATTAAAATGAAAATATTCCTTTAGAGAAATATATGGAAGGTTTATTA
*
298363 AAACATTATATCTTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCAATTTCC
66 AAACATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCAATTTCC
* *
298421 TTTTATATAATATATCATATTAAAATGGAAATATTCCTTTAAAGAAATATATGGAAGGTTTATTA
1 TTTTATATAATATATCATATTAAAATGAAAATATTCCTTTAGAGAAATATATGGAAGGTTTATTA
*
298486 AAACATTATATCCTTTCCGAAAGGATATTAACTTCCATG-TTTTAATATT
66 AAACATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATT
298535 TAACGAAATC
Statistics
Matches: 218, Mismatches: 17, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
122 122 0.56
123 96 0.44
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.43
Consensus pattern (123 bp):
TTTTATATAATATATCATATTAAAATGAAAATATTCCTTTAGAGAAATATATGGAAGGTTTATTA
AAACATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCAATTTCC
Done.